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- PDB-9dzd: PvRBP2b N-terminal domain stabilised mutant WHT2484 -

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Basic information

Entry
Database: PDB / ID: 9dzd
TitlePvRBP2b N-terminal domain stabilised mutant WHT2484
ComponentsReticulocyte-binding protein 2b
KeywordsCELL ADHESION / Malaria / Red Blood Cell / Reticulocyte Binding Protein
Function / homologyNBD94 domain / Nucleotide-Binding Domain 94 of RH / DI(HYDROXYETHYL)ETHER / Reticulocyte-binding protein 2b
Function and homology information
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPymm, P. / D Sa, J. / Tham, W.H.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)2016908 Australia
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Stabilized designs of the malaria adhesin protein PvRBP2b for use as a potential diagnostic for Plasmodium vivax.
Authors: D Sa, J. / Krauss, L. / Smith, L. / D'Andrea, L. / Chan, L.J. / Abraham, A. / Kiernan-Walker, N. / Mazhari, R. / Lamont, M. / Lim, P.S. / Sattabongkot, J. / Lacerda, M.V. / Wini, L. / ...Authors: D Sa, J. / Krauss, L. / Smith, L. / D'Andrea, L. / Chan, L.J. / Abraham, A. / Kiernan-Walker, N. / Mazhari, R. / Lamont, M. / Lim, P.S. / Sattabongkot, J. / Lacerda, M.V. / Wini, L. / Mueller, I. / Longley, R.J. / Pymm, P. / Fleishman, S.J. / Tham, W.H.
History
DepositionOct 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Reticulocyte-binding protein 2b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1536
Polymers39,6781
Non-polymers4745
Water5,423301
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.423, 46.423, 361.005
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-763-

HOH

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Components

#1: Protein Reticulocyte-binding protein 2b


Mass: 39678.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U4ERT5
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10 % Propan-2-ol 10 % PEG MME 5000 0.1 M Na Cacodylate pH 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953647 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953647 Å / Relative weight: 1
ReflectionResolution: 1.85→46.04 Å / Num. obs: 35632 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 1 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.023 / Rrim(I) all: 0.082 / Χ2: 1.02 / Net I/σ(I): 19.5 / Num. measured all: 450878
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 13.4 % / Rmerge(I) obs: 1.513 / Num. unique obs: 2099 / CC1/2: 0.792 / Rpim(I) all: 0.423 / Χ2: 1.03

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→46.04 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2216 1999 5.64 %
Rwork0.189 --
obs0.1909 35466 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→46.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2530 0 31 301 2862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.817
X-RAY DIFFRACTIONf_dihedral_angle_d14.4141014
X-RAY DIFFRACTIONf_chiral_restr0.048378
X-RAY DIFFRACTIONf_plane_restr0.007449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.39821370.32522283X-RAY DIFFRACTION100
1.9-1.950.33731400.27172352X-RAY DIFFRACTION100
1.95-20.28451390.21912320X-RAY DIFFRACTION100
2-2.070.23991390.20222334X-RAY DIFFRACTION100
2.07-2.140.23281390.19372321X-RAY DIFFRACTION100
2.14-2.230.23651410.1932365X-RAY DIFFRACTION100
2.23-2.330.23911410.18812375X-RAY DIFFRACTION100
2.33-2.450.241410.18422362X-RAY DIFFRACTION100
2.45-2.610.2361410.18852359X-RAY DIFFRACTION100
2.61-2.810.2251420.19272367X-RAY DIFFRACTION100
2.81-3.090.20621440.19652432X-RAY DIFFRACTION100
3.09-3.540.24011460.18262417X-RAY DIFFRACTION100
3.54-4.460.19191480.16352484X-RAY DIFFRACTION100
4.46-46.040.19391610.18682696X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 15.595 Å / Origin y: 5.2983 Å / Origin z: -27.0285 Å
111213212223313233
T0.1422 Å20.0284 Å2-0.0087 Å2-0.134 Å2-0.0001 Å2--0.232 Å2
L0.5939 °20.2148 °2-0.5781 °2-0.8999 °2-1.0409 °2--3.6495 °2
S0.0126 Å °-0.0087 Å °0.0262 Å °-0.003 Å °0.0102 Å °-0.0292 Å °-0.0379 Å °0.0604 Å °-0.0306 Å °
Refinement TLS groupSelection details: all

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